32NZ | pdb_000032nz

An activating H90 ScFv bound to the hyaluronan-binding domain of human CD44

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4H0H
experimental model	PDB	4PZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	100 mM HEPES, 1% PEG 2000 MME, 1 M succinic acid

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.538	α = 90
b = 92.538	β = 90
c = 109.333	γ = 90

Symmetry
Space Group	P 41 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2021-07-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.8	56.15	100	0.095	0.097	0.02	1	20.5	44.8		44688

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.84	100		5.087	5.272	1.354	0.414	0.4	27.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1.8	56.21	44611	2228	99.982	0.196	0.1941	0.2042	0.24	0.2479	RANDOM	45.122

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-1.271			-1.271		2.543

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.276
r_dihedral_angle_3_deg	12.489
r_dihedral_angle_2_deg	10.631
r_lrange_other	9.681
r_lrange_it	9.647
r_dihedral_angle_1_deg	7.666
r_scangle_it	6.94
r_scangle_other	6.939
r_mcangle_it	6.3
r_mcangle_other	6.299
r_scbond_it	4.725
r_scbond_other	4.725
r_mcbond_it	4.363
r_mcbond_other	4.358
r_angle_refined_deg	1.414
r_angle_other_deg	0.496
r_nbd_refined	0.208
r_symmetry_nbd_other	0.201
r_nbtor_refined	0.179
r_symmetry_xyhbond_nbd_refined	0.163
r_xyhbond_nbd_refined	0.16
r_nbd_other	0.135
r_symmetry_nbd_refined	0.11
r_symmetry_nbtor_other	0.085
r_symmetry_xyhbond_nbd_other	0.082
r_chiral_restr	0.074
r_metal_ion_refined	0.062
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2863
Nucleic Acid Atoms
Solvent Atoms	261
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing